getBackgroundFrequencies: Get the four nucleotides background frequencies

In PWMEnrich: PWM enrichment analysis

Description

Estimate the background frequencies of A,C,G,T on a set of promoters from an organism

Usage

getBackgroundFrequencies(organism = "dm3", pseudo.count = 1, quick = FALSE)

Arguments

organism	either a name of the organisms for which the background should be compiled (supported names are "dm3", "mm9" and "hg19"), a BSgenome object, DNAStringSet, or list of DNAString objects
pseudo.count	the number to which the frequencies sum up to, by default 1
quick	if to preform fitting on a reduced set of 100 promoters. This will not give as good results but is much quicker than fitting to all the promoters (~10k). Usage of this parameter is recommended only for testing and rough estimates.

Author(s)

Robert Stojnic, Diego Diez

Examples

## Not run: 
  getBackgroundFrequencies("dm3")

## End(Not run)

PWMEnrich documentation built on Nov. 8, 2020, 7:45 p.m.